Change adjustment from pixel to microns

[Erup]

Dear Qupath-Group,

I want to change the adjustment of the measurement and magnification. After I installed the program I only can use pixel to describe the area of the picture. For my work I need microns as scale unit.

Please, can anybody help me? I hope there is a trick. :)

Erup

[micros...@gmail.com]

The measurement and magnification in QuPath are read from the metadata in the image file, so if QuPath is not picking it up, either the metadata is in a format it cannot read, or the metadata is not there to process.

If the metadata is there and is not being found, one possibility is that you could add the Bioformats extension, instructions here: https://github.com/qupath/qupath-bioformats-extension

If the metadata does not exist, you will need to either add that through ImageJ or another program.  ImageJ can be accessed through QuPath using the Extensions menu.

If you could provide further information on what your image file type is, I might be able to be more specific.

[Cristina Miranda]

I have the same problem.. 

My image file format is .TIF

Can I have more information about how to change the adjustment of the measurement and magnification? 

Thank you!! 

[micros...@gmail.com]

As far as I can tell, those parameters are not easily accessible through scripting.  I could be wrong, but I run into errors trying to use "setMagnification" and I could not find anything for setPixelWidthMicrons() or similar.

I recommend VIPS or ImageJ/FIJI to make sure your image has the correct metadata before starting with QuPath.
Here is an example of opening a TIFF file in ImageJ and editing the image properties to put the appropriate pixel size.  Note that the "Unit of length" has not yet been changed.

[Cristina Miranda]

Ok! Thank you! 

I also wonder if it is possible to change my scalebar which is in pixels to microns? 

[micros...@gmail.com]

Usually the scalebar will automatically use microns as long as the pixel sizes are listed in the image metadata. If you do not have the metadata set, QuPath would have no way of knowing how to set the bar size. Have you gotten the pixel sizes added to your image yet?